Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Ubiquitin-specific protease 48 drives malignant progression of colorectal cancer by suppressing autophagy through stabilizing sequestosome 1

Cell Death & Differentiation (2025)Cite this article

Subjects

Abstract

Colorectal cancer (CRC) is the third malignant tumor in incidence rate and the second leading cause of cancer death worldwide. The progression of CRC is associated with both autophagy and ubiquitin-specific proteases (USPs). While USPs have been shown to regulate autophagy, their specific involvement in CRC autophagy remains largely unexplored. Herein, through the analysis of autophagy-related protein expression levels and proteomics, we found that high expression of USP48 was closely related to the inhibition of autophagy in CRC. And further analysis of CRC tissues showed that USP48 served as an independent risk factor for CRC patient prognosis. In vitro, we observed that USP48 significantly enhanced the proliferative, migration and invasion capacities of CRC cells. In vivo experiments showed that USP48 knockdown significantly inhibited the growth of subcutaneous tumors in nude mice, and the deletion of USP48 in intestinal epithelial cells reduced the number of intestinal tumors and mortality rate of mice. Mechanistically, USP48 was found to interact with the autophagy substrate protein sequestosome 1 (SQSTM1) and induce its deubiquitination at K420. This process inhibited autophagy, consequently maintaining the protein stability of SQSTM1. Rescue experiments demonstrated that SQSTM1 was the key target for USP48 to inhibit autophagy and promote CRC progression. Based on these findings, we constructed a tetrahedral DNA nanomaterial loaded with USP48 small interfering RNA (siRNA), which could effectively inhibited the progression of CRC in vivo while exhibiting excellent biocompatibility. In summary, our findings highlighted the role of USP48 in promoting CRC progression via the stabilization of SQSTM1, which leads to the suppression of autophagy. Thus, USP48 may be a potential therapeutic target for CRC.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: The elevated USP48 negatively correlates with autophagy activity and can predict poor prognosis of CRC.
Fig. 2: USP48 promotes the progression of CRC in vitro and in vivo.
Fig. 3: USP48 interacts with autophagy substrate SQSTM1.
Fig. 4: USP48 suppresses the degradation of SQSTM1 through restraining autophagy.
Fig. 5: USP48 catalyzes K63-linked deubiquitination of SQSTM1 at K420.
Fig. 6: USP48 inhibits autophagy and promotes CRC progression through stabilizing SQSTM1.
Fig. 7: Nanomaterial-loaded USP48 siRNA inhibits the development of CRC.
Fig. 8: A schematic diagram illustrating the mechanism of USP48 in CRC.

Similar content being viewed by others

Data availability

All data generated or analyzed in this study are available in this article and its Supplementary Files.

References

  1. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71:209–49.

    PubMed  Google Scholar 

  2. Morris VK, Kennedy EB, Baxter NN, Benson AB 3rd, Cercek A, et al. Treatment of metastatic colorectal cancer: ASCO guideline. J Clin Oncol Off J Am Soc Clin Oncol. 2023;41:678–700.

    Article  Google Scholar 

  3. Luo XJ, Zhao Q, Liu J, Zheng JB, Qiu MZ, Ju HQ, et al. Novel genetic and epigenetic biomarkers of prognostic and predictive significance in stage II/III colorectal cancer. Mol Ther J Am Soc Gene Ther. 2021;29:587–96.

    Article  CAS  Google Scholar 

  4. Zhang X, Sun H, Chen W, He X. Elevated expression of AGGF1 predicts poor prognosis and promotes the metastasis of colorectal cancer. BMC Cancer. 2019;19:1252.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Korver SK, Gibson RJ, Bowen JM, Coller JK. Toll-like receptor/interleukin-1 domain innate immune signalling pathway genetic variants are candidate predictors for severe gastrointestinal toxicity risk following 5-fluorouracil-based chemotherapy. Cancer Chemother Pharmacol. 2019;83:217–36.

    Article  CAS  PubMed  Google Scholar 

  6. Liu S, Yao S, Yang H, Liu S, Wang Y. Autophagy: regulator of cell death. Cell Death Dis. 2023;14:648.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Eskelinen EL. Autophagy: supporting cellular and organismal homeostasis by self-eating. Int J Biochem Cell Biol. 2019;111:1–10.

    Article  CAS  PubMed  Google Scholar 

  8. Feng X, Zhang H, Meng L, Song H, Zhou Q, Qu C, et al. Hypoxia-induced acetylation of PAK1 enhances autophagy and promotes brain tumorigenesis via phosphorylating ATG5. Autophagy. 2021;17:723–42.

    Article  CAS  PubMed  Google Scholar 

  9. Marsh T, Debnath J. Autophagy suppresses breast cancer metastasis by degrading NBR1. Autophagy. 2020;16:1164–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Li X, Dai Z, Wu X, Zhang N, Zhang H, Wang Z, et al. The comprehensive analysis identified an autophagy signature for the prognosis and the immunotherapy efficiency prediction in lung adenocarcinoma. Front Immunol. 2022;13:749241.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Liu M, Sun T, Li N, Peng J, Fu D, Li W, et al. BRG1 attenuates colonic inflammation and tumorigenesis through autophagy-dependent oxidative stress sequestration. Nat Commun. 2019;10:4614.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Haruki K, Kosumi K, Hamada T, Twombly TS, Väyrynen JP, Kim SA, et al. Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer. J Pathol. 2020;250:397–408.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Qureshi-Baig K, Kuhn D, Viry E, Pozdeev VI, Schmitz M, Rodriguez F, et al. Hypoxia-induced autophagy drives colorectal cancer initiation and progression by activating the PRKC/PKC-EZR (ezrin) pathway. Autophagy. 2020;16:1436–52.

    Article  CAS  PubMed  Google Scholar 

  14. Li W, Zhou C, Yu L, Hou Z, Liu H, Kong L, et al. Tumor-derived lactate promotes resistance to bevacizumab treatment by facilitating autophagy enhancer protein RUBCNL expression through histone H3 lysine 18 lactylation (H3K18la) in colorectal cancer. Autophagy. 2024;20:114–30.

    Article  CAS  PubMed  Google Scholar 

  15. Hu M, Li P, Li M, Li W, Yao T, Wu JW, et al. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell. 2002;111:1041–54.

    Article  CAS  PubMed  Google Scholar 

  16. Kitamura H. Ubiquitin-specific proteases (USPs) and metabolic disorders. Int J Mol Sci. 2023;24. https://doi.org/10.3390/ijms24043219.

  17. Choi BJ, Park SA, Lee SY, Cha YN, Surh YJ. Hypoxia induces epithelial-mesenchymal transition in colorectal cancer cells through ubiquitin-specific protease 47-mediated stabilization of snail: a potential role of Sox9. Sci Rep. 2017;7:15918.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Xiao Y, Jiang X, Yin K, Miao T, Lu H, Wang W, et al. USP35 promotes cell proliferation and chemotherapeutic resistance through stabilizing FUCA1 in colorectal cancer. Oncogenesis. 2023;12:12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kim JH, Seo D, Kim SJ, Choi DW, Park JS, Ha J, et al. The deubiquitinating enzyme USP20 stabilizes ULK1 and promotes autophagy initiation. EMBO Rep. 2018;19. https://doi.org/10.15252/embr.201744378.

  20. Raimondi M, Cesselli D, Di Loreto C, La Marra F, Schneider C, Demarchi F. USP1 (ubiquitin specific peptidase 1) targets ULK1 and regulates its cellular compartmentalization and autophagy. Autophagy. 2019;15:613–30.

    Article  CAS  PubMed  Google Scholar 

  21. Thayer JA, Awad O, Hegdekar N, Sarkar C, Tesfay H, Burt C, et al. The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability. Autophagy. 2020;16:140–53.

    Article  CAS  PubMed  Google Scholar 

  22. Gao Z, Li C, Sun H, Bian Y, Cui Z, Wang N, et al. N(6)-methyladenosine-modified USP13 induces pro-survival autophagy and imatinib resistance via regulating the stabilization of autophagy-related protein 5 in gastrointestinal stromal tumors. Cell Death Differ. 2023;30:544–59.

    Article  CAS  PubMed  Google Scholar 

  23. Kim MJ, Min Y, Jeong SK, Son J, Kim JY, Lee JS, et al. USP15 negatively regulates lung cancer progression through the TRAF6-BECN1 signaling axis for autophagy induction. Cell Death Dis. 2022;13:348.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lee Y, Chou TF, Pittman SK, Keith AL, Razani B, Weihl CC. Keap1/Cullin3 modulates p62/SQSTM1 activity via UBA domain ubiquitination. Cell Rep. 2017;19:188–202.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Peng H, Yang J, Li G, You Q, Han W, Li T, et al. Ubiquitylation of p62/sequestosome1 activates its autophagy receptor function and controls selective autophagy upon ubiquitin stress. Cell Res. 2017;27:657–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Amaravadi RK, Kimmelman AC, Debnath J. Targeting autophagy in cancer: recent advances and future directions. Cancer Discov. 2019;9:1167–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Miller DR, Thorburn A. Autophagy and organelle homeostasis in cancer. Dev Cell. 2021;56:906–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Jing Z, He X, Jia Z, Sa Y, Yang B, Liu P. NCAPD2 inhibits autophagy by regulating Ca(2+)/CAMKK2/AMPK/mTORC1 pathway and PARP-1/SIRT1 axis to promote colorectal cancer. Cancer Lett. 2021;520:26–37.

    Article  CAS  PubMed  Google Scholar 

  29. Wei R, Xiao Y, Song Y, Yuan H, Luo J, Xu W. FAT4 regulates the EMT and autophagy in colorectal cancer cells in part via the PI3K-AKT signaling axis. J Exp Clin Cancer Res. 2019;38:112.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Jo YK, Kim SC, Park IJ, Park SJ, Jin DH, Hong SW, et al. Increased expression of ATG10 in colorectal cancer is associated with lymphovascular invasion and lymph node metastasis. PloS ONE. 2012;7:e52705.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Antao AM, Kaushal K, Das S, Singh V, Suresh B, Kim KS, et al. USP48 governs cell cycle progression by regulating the protein level of Aurora B. Int J Mol Sci. 2021;22. https://doi.org/10.3390/ijms22168508.

  32. Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, et al. Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. Nat Commun. 2018;9:2280.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Zhou A, Lin K, Zhang S, Ma L, Xue J, Morris SA, et al. Gli1-induced deubiquitinase USP48 aids glioblastoma tumorigenesis by stabilizing Gli1. EMBO Rep. 2017;18:1318–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lei X, Li X, Chen H, Liu Z. USP48 sustains chemoresistance and metastasis in ovarian cancer. Current Cancer Drug Targets. 2020;20:689–99.

    Article  CAS  PubMed  Google Scholar 

  35. Nezis IP, Stenmark H. p62 at the interface of autophagy, oxidative stress signaling, and cancer. Antioxid Redox Signal. 2012;17:786–93.

    Article  CAS  PubMed  Google Scholar 

  36. Deng Z, Lim J, Wang Q, Purtell K, Wu S, Palomo GM, et al. ALS-FTLD-linked mutations of SQSTM1/p62 disrupt selective autophagy and NFE2L2/NRF2 anti-oxidative stress pathway. Autophagy. 2020;16:917–31.

    Article  CAS  PubMed  Google Scholar 

  37. Gou H, Chen X, Zhu X, Li L, Hou L, Zhou Y, et al. Sequestered SQSTM1/p62 crosstalk with Keap1/NRF2 axis in hPDLCs promotes oxidative stress injury induced by periodontitis. Free Radic Biol Med. 2022;190:62–74.

    Article  CAS  PubMed  Google Scholar 

  38. Pan JA, Sun Y, Jiang YP, Bott AJ, Jaber N, Dou Z, et al. TRIM21 ubiquitylates SQSTM1/p62 and suppresses protein sequestration to regulate redox homeostasis. Mol Cell. 2016;61:720–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Song P, Li S, Wu H, Gao R, Rao G, Wang D, et al. Parkin promotes proteasomal degradation of p62: implication of selective vulnerability of neuronal cells in the pathogenesis of Parkinson’s disease. Protein Cell. 2016;7:114–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA functional materials assembled from branched DNA: design, synthesis, and applications. Chem Rev. 2020;120:9420–81.

    Article  CAS  PubMed  Google Scholar 

  41. Jiang Q, Liu S, Liu J, Wang ZG, Ding B. Rationally designed DNA-origami nanomaterials for drug delivery in vivo. Adv Mater. 2019;31:e1804785.

    Article  PubMed  Google Scholar 

  42. Wang D, Zhang X, Zhu X. Drug-grafted DNA for cancer therapy. J Phys Chem B. 2023;127:5379–88.

    Article  CAS  PubMed  Google Scholar 

  43. Guo W, Gao H, Li H, Ge S, Zhang F, Wang L, et al. Self-assembly of a multifunction DNA tetrahedron for effective delivery of aptamer PL1 and Pcsk9 siRNA potentiate immune checkpoint therapy for colorectal cancer. ACS Appl Mater Interfaces. 2022;14:31634–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Dai B, Hu Y, Duan J, Yang XD. Aptamer-guided DNA tetrahedron as a novel targeted drug delivery system for MUC1-expressing breast cancer cells in vitro. Oncotarget. 2016;7:38257–69.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Zhao Y, Xu J, Le VM, Gong Q, Li S, Gao F, et al. EpCAM aptamer-functionalized cationic liposome-based nanoparticles loaded with miR-139-5p for targeted therapy in colorectal cancer. Mol Pharm. 2019;16:4696–710.

    Article  CAS  PubMed  Google Scholar 

  46. Pishavar E, Yazdian-Robati R, Abnous K, Hashemi M, Ebrahimian M, Feizpour R, et al. Aptamer-functionalized mesenchymal stem cells-derived exosomes for targeted delivery of SN38 to colon cancer cells. Iran J Basic Med Sci. 2023;26:388–94.

    PubMed  PubMed Central  Google Scholar 

Download references

Funding

This research was supported by grant from the National Natural Science Foundation of China (82122041, 82472357 and 82202604), the Key Research and Development Program of Shandong Province (2021ZLGX02, 2020CXGC011304 and 2022CXGC020507), Fundamental Research Funds for the Central Universities (2022JC002), Natural Science Foundation of Shandong Province (ZR2022QH044), Taishan Scholars Climbing Program of Shandong Province (NO.tspd20210323), Young Taishan Scholars Program of Shandong Province (NO.tsqn201909176, NO.tsqn202211322 and NO.tsqn202211323), Outstanding Young and Middle-aged Scholar of Shandong University and Tumor Biomarker Innovation Team Foundation of Jinan City (2021GXRC020).

Author information

Author notes

  1. These authors contributed equally: Juan Li, Aijing Liu, Weili Duan.

Authors and Affiliations

  1. Department of Clinical Laboratory, The Second Qilu Hospital of Shandong University, Jinan, Shandong, China

    Juan Li, Aijing Liu, Weili Duan, Yanru Li, Xue Kong, Dun Niu, Shaojun Liu, Peng Zhang, Chuanxin Wang & Peilong Li

  2. Department of Clinical Laboratory, Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Qilu Hospital of Shandong University, Jinan, Shandong, China

    Tiantian Wang & Lutao Du

  3. Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China

    Chuanxin Wang

  4. Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Jinan, Shandong, China

    Lutao Du

Authors
  1. Juan Li
    View author publications

    Search author on:PubMed Google Scholar

  2. Aijing Liu
    View author publications

    Search author on:PubMed Google Scholar

  3. Weili Duan
    View author publications

    Search author on:PubMed Google Scholar

  4. Yanru Li
    View author publications

    Search author on:PubMed Google Scholar

  5. Xue Kong
    View author publications

    Search author on:PubMed Google Scholar

  6. Tiantian Wang
    View author publications

    Search author on:PubMed Google Scholar

  7. Dun Niu
    View author publications

    Search author on:PubMed Google Scholar

  8. Shaojun Liu
    View author publications

    Search author on:PubMed Google Scholar

  9. Peng Zhang
    View author publications

    Search author on:PubMed Google Scholar

  10. Chuanxin Wang
    View author publications

    Search author on:PubMed Google Scholar

  11. Peilong Li
    View author publications

    Search author on:PubMed Google Scholar

  12. Lutao Du
    View author publications

    Search author on:PubMed Google Scholar

Contributions

CW, PL, and LD designed and supervised this study; JL, AL, and WD executed the development of experiments, statistical analysis and writing; YL, XK, TW, DN, and SL participated in the experiments and collected data; PZ provided technical support. All authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Chuanxin Wang, Peilong Li or Lutao Du.

Ethics declarations

Competing interests

The authors declare no competing interests.

Ethics approval

This study was approved by the Ethics Committee of the Second Hospital of Shandong University and the Ethics Committee of Qutdo Biotech.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, J., Liu, A., Duan, W. et al. Ubiquitin-specific protease 48 drives malignant progression of colorectal cancer by suppressing autophagy through stabilizing sequestosome 1. Cell Death Differ (2025). https://doi.org/10.1038/s41418-025-01617-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Version of record:

  • DOI: https://doi.org/10.1038/s41418-025-01617-1

Search

Advanced search

Quick links